[sage-devel] Re: Aliases ? No Aliases ? From Graph.predecessors to neighbors_in

2009-10-09 Thread Nicolas M. Thiery
On Fri, Oct 09, 2009 at 11:36:00AM -0700, Nathann Cohen wrote: > > hmmm In everything I read, there are just mentions of out- > neighbors and in-neighbors. I can give you a hundred references using > these names, Yup. > and I would be much more alarmed to give you one reference using > pre

[sage-devel] Re: Numpy build failure on HP-UX with PA-RISC CPU..

2009-10-09 Thread Jason Grout
Dr. David Kirkby wrote: > I tried to subscribe to the numpy discussion list at > > http://projects.scipy.org/mailman/listinfo/numpy-discussion > > but the server is down. > > Likewise for the projects homepage. It's somewhat difficult to know > where to report this. > > Perhaps if William or

[sage-devel] Numpy build failure on HP-UX with PA-RISC CPU..

2009-10-09 Thread Dr. David Kirkby
I tried to subscribe to the numpy discussion list at http://projects.scipy.org/mailman/listinfo/numpy-discussion but the server is down. Likewise for the projects homepage. It's somewhat difficult to know where to report this. Perhaps if William or someone knows the email addresses of one of

[sage-devel] Re: Serious issues the way doctest failures are handled.

2009-10-09 Thread Dr. David Kirkby
Dr. David Kirkby wrote: > I've just tried the patch at > > http://sagetrac.org/sage_trac/ticket/6788 > > It does not appear to have solved my problem, but it highlights one that > has bugged me for some time - one where running doctests can bring the > machine to an almost standstill. I did n

[sage-devel] Re: need help related to conversion maxima code into Sage

2009-10-09 Thread ma...@mendelu.cz
Thanks, thats incredibly fast. I have now error when trying to download the patch. I'll try it as soon as possible. The last version od desolvers.py is http://user.mendelu.cz/marik/temp/desolvers.py Robert M. On 9 říj, 18:25, kcrisman wrote: > See patch at #385.  Can you test it with your new

[sage-devel] Re: Doctest fails for Biopython-1.52.spkg

2009-10-09 Thread MaxTheMouse
On Oct 9, 10:24 pm, Marshall Hampton wrote: > One alternative would be to patch the test_Wise.py file so that > instead of > > self.assert_(sys.stdout.getvalue().startswith("dnal -kbyte 10 > seq1.fna seq2.fna")) > > within test_dnal we'd have > > self.assert_(sys.stdout.getvalue().startswit

[sage-devel] Re: Doctest fails for Biopython-1.52.spkg

2009-10-09 Thread Marshall Hampton
One alternative would be to patch the test_Wise.py file so that instead of self.assert_(sys.stdout.getvalue().startswith("dnal -kbyte 10 seq1.fna seq2.fna")) within test_dnal we'd have self.assert_(sys.stdout.getvalue().startswith("dnal -kbyte 10") and similarly for test_psw. That wou

[sage-devel] Re: Aliases ? No Aliases ? From Graph.predecessors to neighbors_in

2009-10-09 Thread Nathann Cohen
hmmm In everything I read, there are just mentions of out- neighbors and in-neighbors. I can give you a hundred references using these names, and I would be much more alarmed to give you one reference using predecessors and successors... Especially when for edges, you can type out and in to k

[sage-devel] Re: sagemath infrastructure scheduled downtime

2009-10-09 Thread Robert Bradshaw
On Oct 9, 2009, at 9:55 AM, Jason Grout wrote: > Jason Grout wrote: >> Rob Beezer wrote: >>> I'm able to log-in to Trac, but get >>> >>> Trac detected an internal error: >>> TimeoutError: Unable to get database connection within 20 seconds >>> >>> when I try to view a ticket. Sounds like Minh is

[sage-devel] Re: Aliases ? No Aliases ? From Graph.predecessors to neighbors_in

2009-10-09 Thread Robert Bradshaw
On Oct 9, 2009, at 7:11 AM, Nicolas M. Thiery wrote: > On Thu, Oct 08, 2009 at 07:03:29PM -0700, Tom Boothby wrote: >> +1 to deprecation >> >> On Thu, Oct 8, 2009 at 5:43 PM, Jason Grout > s...@creativetrax.com> wrote: >>> >>> Nathann Cohen wrote: Hello everybody !!! Following

[sage-devel] Re: sagemath infrastructure scheduled downtime

2009-10-09 Thread Jason Grout
Jason Grout wrote: > Rob Beezer wrote: >> I'm able to log-in to Trac, but get >> >> Trac detected an internal error: >> TimeoutError: Unable to get database connection within 20 seconds >> >> when I try to view a ticket. Sounds like Minh is having a similar >> problem. >> >> Rob > > I can see ti

[sage-devel] Re: sagemath infrastructure scheduled downtime

2009-10-09 Thread Jason Grout
Rob Beezer wrote: > I'm able to log-in to Trac, but get > > Trac detected an internal error: > TimeoutError: Unable to get database connection within 20 seconds > > when I try to view a ticket. Sounds like Minh is having a similar > problem. > > Rob I can see tickets okay, but it's taking aro

[sage-devel] Re: need help related to conversion maxima code into Sage

2009-10-09 Thread kcrisman
On Oct 9, 9:26 am, kcrisman wrote: > On Oct 9, 7:46 am, "ma...@mendelu.cz" wrote: > > > > > > > Hello, > > > trying to fix desolve_laplace as described > > athttp://groups.google.cz/group/sage-support/browse_thread/thread/b6f6b... > > > It is continuation of tickethttp://trac.sagemath.org/sag

[sage-devel] Doctest fails for Biopython-1.52.spkg

2009-10-09 Thread MaxTheMouse
Hi all, I am playing around with the new biopython spkg (1.52). In particular, I would like to have a spkg-check script to run the included tests. This mostly works and the test skips testing modules that are not installed. I am having one problem however. I get a failure with one test.

[sage-devel] Re: Categories restart: call for reviewers

2009-10-09 Thread Nicolas M. Thiery
On Fri, Oct 09, 2009 at 12:25:54AM -0700, Robert Bradshaw wrote: > > Robert: What's your time line for: > > - the review of categories-fixsagelib-nt.patch > > - finalizing #5597 [with patch, needs work] rename coercion action > > methods > > Rebased, has doctests, needs review. Yep. Will rev

[sage-devel] Re: sagemath infrastructure scheduled downtime

2009-10-09 Thread Rob Beezer
I'm able to log-in to Trac, but get Trac detected an internal error: TimeoutError: Unable to get database connection within 20 seconds when I try to view a ticket. Sounds like Minh is having a similar problem. Rob On Oct 8, 8:49 pm, William Stein wrote: > OK, everything is done.  Please repo

[sage-devel] Re: Aliases ? No Aliases ? From Graph.predecessors to neighbors_in

2009-10-09 Thread Nicolas M. Thiery
On Thu, Oct 08, 2009 at 07:03:29PM -0700, Tom Boothby wrote: > +1 to deprecation > > On Thu, Oct 8, 2009 at 5:43 PM, Jason Grout > wrote: > > > > Nathann Cohen wrote: > >> Hello everybody !!! > >> > >> Following > >> http://groups.google.com/group/sage-devel/browse_thread/thread/bfeb9b1828a0435

[sage-devel] Re: solve command - what is actually passed to maxima?

2009-10-09 Thread Jason Grout
kcrisman wrote: > > I have to say, this output is not trivial to understand, though. > - kcrisman It takes a bit of reading and putting things together to understand it, but it is the definitive answer to the question: "Where can i dig out the string which actually is passed to Maxima?" (tho

[sage-devel] Re: need help related to conversion maxima code into Sage

2009-10-09 Thread kcrisman
On Oct 9, 7:46 am, "ma...@mendelu.cz" wrote: > Hello, > > trying to fix desolve_laplace as described > athttp://groups.google.cz/group/sage-support/browse_thread/thread/b6f6b... > > It is continuation of tickethttp://trac.sagemath.org/sage_trac/ticket/6479 > which has been (hope) solved. > > T

[sage-devel] Re: solve command - what is actually passed to maxima?

2009-10-09 Thread kcrisman
On Oct 9, 7:13 am, Jason Grout wrote: > ma...@mendelu.cz wrote: > > > I was not able to find these informations in documentation. Should > > this be documented? Or is this trivial thing for skilled programers in > > Python? > > It should probably be documented somewhere (I don't know if it is).

[sage-devel] need help related to conversion maxima code into Sage

2009-10-09 Thread ma...@mendelu.cz
Hello, trying to fix desolve_laplace as described at http://groups.google.cz/group/sage-support/browse_thread/thread/b6f6b6f056e80149/e2c0cf18cce9926c It is continuation of ticket http://trac.sagemath.org/sage_trac/ticket/6479 which has been (hope) solved. The temporary code is http://user.mend

[sage-devel] Re: solve command - what is actually passed to maxima?

2009-10-09 Thread Jason Grout
ma...@mendelu.cz wrote: > > I was not able to find these informations in documentation. Should > this be documented? Or is this trivial thing for skilled programers in > Python? It should probably be documented somewhere (I don't know if it is). A google search for "sage log pexpect" yields t

[sage-devel] Re: Categories restart: call for reviewers

2009-10-09 Thread Robert Bradshaw
On Sep 16, 2009, at 5:49 AM, Nicolas M. Thiery wrote: > > Dear category fans, > > Thanks to Florent (and previous work by Anne, Jason, Franco, ...) all > the sage-combinat related categories have a positive review. There > remains just the mostly trivial categories listed below which would